According to the JVM manual, the process is:
- Set the amp to the desired channel, mode, etc.
- Press the MIDI button twice, the light should start flashing
- Select the preset on the PBC you wish to assign those settings to
- The light should stop flashing at this point.
Is this the process you were trying? If so, then the JVM is probably sent to the wrong channel. We'll have to reassign it.
FYI, the PBC is unable to detect what's connected to it - generally speaking, MIDI doesn't work that way (unfortunately). You have to tell it what's connected so that it knows what messages to send. However, the default settings for the PBC (a Mini Amp Gizmo on MIDI channel 1) should be good enough to get started.